Population genomics of wild and laboratory zebrafish (Danio rerio)

Abstract

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST-based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among-clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low FST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

“…Results (see Figure S5) identified 14 SNPs that were shared across all our strains and all fish of haplogroup 1 but were absent from all haplogroups 2 and 3, showing that NA, WIK, EKW, and CB all derived from haplogroup 1 (Whiteley et al 2011). Among the six strains we used and the 16 populations in the Whiteley et al (2011) study, only AB appeared in both studies, and in both cases was in haplogroup 1. We conclude that our samples represent a single branch of the broad diversity of mitochondrial lineages across the zebrafish species.…”

“…Analysis of the mitochondrial genome-encoded cytb gene showed that our strains all derived from mitochondrial haplogroup 1, suggesting that a broader understanding of the genetics of sex determination across the full diversity of zebrafish will require investigations of haplogroups 2 and 3 (populations in Nepal and Southern India, respectively), which diverged from haplogroup 1 about 3 million years ago (Whiteley et al 2011). Investigations of Danio species closely related to zebrafish will also add to our understanding, although the sar4 sexdetermination locus may not be widely conserved with other danios.…”

“…Zebrafish populations collected widely across India fall into three major clades: haplogroup 1 in Northern India and Eastern and Western Nepal, haplogroup 2 in Bangladesh and Southern India, and haplogroup 3 in Central Nepal (Whiteley et al 2011). Infrequent mitochondrial genome contamination in RAD-tag libraries allowed us to reconstruct the cytb locus and assign populations to mitochondrial clades (accession nos.…”

“…We collected RAD-tag genomic data from dwarf danio (D. nigrofasciatus), one of the closest extant relatives of zebrafish, for use as outgroup (Mayden et al 2007;Tang et al 2010). Because D. nigrofasciatus is native to the Sittang basin in Myanmar, which is far outside the range of D. rerio ( Figure S4), the two species are not sympatric (Engeszer et al 2007;Whiteley et al 2011). Analysis utilized 888 kb of sequence from 9442 RAD-tags present in all six D. rerio strains, including 58,282 variable positions of which 51,444 SNPs were parsimony informative.…”

The mind, the lab, and the field: Three kinds of populations in scientific practice

“…Pritchard et al (2000) use three examples: simulated data, data sampled from three geographically distinct groups of Taita Thrush, and data from African and European humans. Thus, the genetic data used by Structure might come from theoretical populations (e.g., simulations), laboratory populations (e.g., Whiteley et al, 2011), or natural populations. Structure uses genetic data to estimate populations.…”